PhosContext2vec: a distributed representation of residue-level sequence contexts and its application to general and kinase-specific phosphorylation site prediction

PhosphoPredict: A bioinformatics tool for prediction of human kinase-specific phosphorylation substrates and sites by integrating heterogeneous feature selection

(2017) Jiangning Song et al.   Scientific Reports

Predicting the errors of predicted local backbone angles and non-local solvent- accessibilities of proteins by deep neural networks

(2016) Jianzhao Gao et al.   BIOINFORMATICS

Sixty-five years of the long march in protein secondary structure prediction: the final stretch?

(2016) Yuedong Yang et al.   BRIEFINGS IN BIOINFORMATICS

DAPPLE 2: a Tool for the Homology-Based Prediction of Post-Translational Modification Sites

(2016) Brett Trost et al.   JOURNAL OF PROTEOME RESEARCH

GlycoMine: a machine learning-based approach for predicting N-, C- and O-linked glycosylation in the human proteome

(2015) Fuyi Li et al.   BIOINFORMATICS

Improving prediction of secondary structure, local backbone angles and solvent accessible surface area of proteins by iterative deep learning

(2015) Rhys Heffernan et al.   Scientific Reports

Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics

(2015) Ehsaneddin Asgari et al.   PLoS One

PhosphoSVM: prediction of phosphorylation sites by integrating various protein sequence attributes with a support vector machine

(2014) Yongchao Dou et al.   AMINO ACIDS

PhosphoPICK: modelling cellular context to map kinase-substrate phosphorylation events

(2014) Ralph Patrick et al.   BIOINFORMATICS

DISOPRED3: precise disordered region predictions with annotated protein-binding activity

(2014) David T. Jones et al.   BIOINFORMATICS

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Accurate in silico identification of species-specific acetylation sites by integrating protein sequence-derived and functional features

(2014) Yuan Li et al.   Scientific Reports

Cascleave 2.0, a new approach for predicting caspase and granzyme cleavage targets

(2013) Mingjun Wang et al.   BIOINFORMATICS

Scalable web services for the PSIPRED Protein Analysis Workbench

(2013) Daniel W. A. Buchan et al.   NUCLEIC ACIDS RESEARCH

From protein sequence to dynamics and disorder with DynaMine

(2013) Elisa Cilia et al.   Nature Communications

TANGLE: Two-Level Support Vector Regression Approach for Protein Backbone Torsion Angle Prediction from Primary Sequences

(2012) Jiangning Song et al.   PLoS One

L1pred: A Sequence-Based Prediction Tool for Catalytic Residues in Enzymes with the L1-logreg Classifier

(2012) Yongchao Dou et al.   PLoS One

PROSPER: An Integrated Feature-Based Tool for Predicting Protease Substrate Cleavage Sites

(2012) Jiangning Song et al.   PLoS One

A Mechanism for the Evolution of Phosphorylation Sites

(2011) Samuel M. Pearlman et al.   CELL

Cascleave: towards more accurate prediction of caspase substrate cleavage sites

(2010) Jiangning Song et al.   BIOINFORMATICS

A comparative study of conservation and variation scores

(2010) Fredrik Johansson et al.   BMC BIOINFORMATICS

Musite, a Tool for Global Prediction of General and Kinase-specific Phosphorylation Sites

(2010) Jianjiong Gao et al.   MOLECULAR & CELLULAR PROTEOMICS

Phospho.ELM: a database of phosphorylation sites--update 2011

(2010) H. Dinkel et al.   NUCLEIC ACIDS RESEARCH

RegPhos: a system to explore the protein kinase–substrate phosphorylation network in humans

(2010) Tzong-Yi Lee et al.   NUCLEIC ACIDS RESEARCH

GPS 2.1: enhanced prediction of kinase-specific phosphorylation sites with an algorithm of motif length selection

(2010) Y. Xue et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis

(2010) J. V. Olsen et al.   Science Signaling

PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update

(2009) Pawel Durek et al.   NUCLEIC ACIDS RESEARCH

GPS 2.0, a Tool to Predict Kinase-specific Phosphorylation Sites in Hierarchy

(2008) Yu Xue et al.   MOLECULAR & CELLULAR PROTEOMICS

PhosphoPep—a database of protein phosphorylation sites in model organisms

(2008) Bernd Bodenmiller et al.   NATURE BIOTECHNOLOGY

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH